Graphene Could Improve DNA Sequencing

Graphene Could Improve DNA Sequencing

Layers of graphene that are only as thick as an atom could help make human DNA sequencing faster and cheaper. Harvard University and MIT researchers have shown that sheets of graphene could be a big improvement over membranes that are currently used for nanopore sequencing–a technique that promises to speed up and simplify the sequencing of long strands of DNA.

Today’s sequencing techniques involve chopping up DNA, making many copies of the pieces, and reading fluorescent molecules attached to them. This approach takes days and costs tens of thousands of dollars. In contrast, nanopore sequencing could, in theory, parse an entire human genome in a few hours.

Nanopore sequencing involves pulling a DNA strand through a tiny hole in a membrane that’s suspended in a salt solution with a voltage applied across it. Ions moving from one side of the membrane to the other create an electric current. As each of four different DNA bases passes through the pore, the current strength decreases to a different extent, making it possible to rapidly sequence the bases.

The nanopores currently used for DNA sequencing are typically made from bacterial proteins or are etched in silicon-nitride membranes. Such membranes are 20 to 30 nanometers thick. But since the distance between two DNA bases is 0.5 nanometers, 40 to 60 bases could be stuck in the pore at a time.

A thinner membrane, such as graphene, might allow for more accurate base identification. A single layer of graphene is just one nanometer thick. It’s “the thinnest membrane that has ever been applied to this problem,” says Jene Golovchenko, a physics professor at Harvard who led the new work, published in Nature this week.

The researchers create their membrane by placing a graphene flake over a 200-nanometer-wide opening in the middle of a silicon-nitride surface. Then they drill a few pores, just nanometers wide, in the graphene with an electron beam. The membrane is finally immersed in a salt solution that’s in contact with silver electrodes. The researchers observed dips in the current when a DNA strand passed through the pore, showing that the method could eventually be used to identify DNA bases.

Two other research groups have demonstrated similar feats recently: one group at the Kavli Institute of Nanoscience and the other at the University of Pennsylvania. These advances were both published in the journal Nano Letters in July.

Identifying individual DNA bases as they pass through the pore will take much more work, however. Each of the four different DNA bases should block the current passing through the pore by a different amount. Any device should be able to distinguish these varying amounts. But doing that will mean precisely controlling the speed with which DNA flies through the pore. Such control is the biggest hurdle to making nanopore sequencing practical.

In the Nature paper, each DNA molecule, containing thousands of bases, passes through the pore in hundreds of microseconds (about four nanoseconds per base). To read a single base, one at a time, would mean the strand would have to be in the pore more than 1,000 times longer, says John Kasianowicz, a biophysicist at the National Institute of Standards and Technology who invented nanopore sequencing. Kasianowicz works with natural membranes and pores made from bacterial proteins. These can hold molecules for tens of milliseconds, but are less stable than silicon nitride and graphene.

“They’ve taken nanopore technology to the next level,” he says of the recent graphene efforts. “Making solid-state nanopores was a great idea, and doctoring them with graphene is a great first step.” But he adds: “To be able to sequence, you need to be able to control the flow of DNA through it and slow it down.”